🎯 Towards tackling the Spectral Bias of Fourier Neural Operators!
Marimuthu Kalimuthu1,2,3, David Holzmüller 4, Mathias Niepert1,2,3,5
1Universität Stuttgart,
2Stuttgart Center for Simulation Science - SimTech,
3International Max Planck Research School for Intelligent Systems (IMPRS-IS),
4INRIA Paris, École Normale Supérieure, PSL University,
5NEC Labs Europe
Published with J2C Certification in Transactions on Machine Learning Research (TMLR, 17.12.2025)
Modeling high-frequency information is a critical challenge in Scientific Machine Learning. For instance, fully turbulent flow simulations of Navier-Stokes equations at Reynolds numbers 3500 and above can generate high-frequency signals due to swirling fluid motions caused by eddies and vortices. Faithfully modeling such signals using neural networks depends on the accurate reconstruction of moderate to high frequencies. However, it has been well known that deep neural nets exhibit the so-called spectral bias toward learning low-frequency components. Meanwhile, Fourier Neural Operators (FNOs) have emerged as a popular class of data-driven models in recent years for solving Partial Differential Equations (PDEs) and for surrogate modeling in general. Although impressive results have been achieved on several PDE benchmark problems, FNOs often perform poorly in learning non-dominant frequencies characterized by local features. This limitation stems from the spectral bias inherent in neural networks and the explicit exclusion of high-frequency modes in FNO and its variants. Therefore, to mitigate these issues and improve FNO’s spectral learning capabilities to represent a broad range of frequency components, we propose two key architectural enhancements: (i) a parallel branch performing local spectral convolutions and (ii) a high-frequency propagation module. Moreover, we propose a novel frequency-sensitive loss term based on radially binned spectral errors. This introduction of a parallel branch for local convolutions reduces the number of trainable parameters by up to 50% while achieving the accuracy of baseline FNO that relies solely on global convolutions. Experiments on three challenging PDE problems in fluid mechanics (Kolmogorov Flow 2D & Turbulent Radiative Layer 3D) and biological pattern formation (Diffusion-Reaction 2D), and the qualitative and spectral analysis of predictions show the effectiveness of our method over the state-of-the-art neural operator baselines.
The core idea of LOGLO-FNO for achieving local spectral convolution in FNO is to first partition or decompose the domain \(D\) into \(M\) non-overlapping hypercubes called patches, such that $$\bigcup_{m=1}^{M} P_m = D,$$ and then performing (learnable) spectral convolutions on these sub-domains without any truncation of Fourier modes.
Because the patches do not overlap and together cover \(D\), their indicator functions \(\chi_{P_m}\) (1 on \(P_m\), 0 elsewhere) form a partition of unity:
Every point of the domain lies in exactly one patch, so a field splits into patch pieces \(\chi_{P_m} u\) that add back up to \(u = \sum_m \chi_{P_m} u\) with no gaps and no point counted twice. The local branch transforms each piece with its own FFT. Point at a patch below to see its indicator, and separate the patches to see the pieces.
Let \(\mathbf{Z} \in \mathbb{R}^{\cdots \times N_c \times N_x \times N_y [\times N_z]}\) be the output of the (initial) lifting layer. Then,
where \(\mathbf{W}_{\square}\) and \(\mathbf{b}_{\square}\) are learnable parameters, and \(\mathcal{K}(\cdot)\) is the global kernel integral.
\[ \mathbf{\Upsilon}_g := ~\sigma \Big[ \mathcal{K}_g(\mathbf{Z}) + \mathbf{W}_{g}*\mathbf{Z} + \mathbf{b}_{g} \Big], \qquad \mathbf{\Upsilon}_l := \sigma \Big[ \mathcal{K}_l(\mathbf{\hat{Z}}) + \mathbf{W}_{l}*\mathbf{\hat{Z}} + \mathbf{b}_{l} \Big], \] \[ \mathcal{L}(\mathbf{Z}, \mathbf{\hat{Z}}, \mathbf{Z^{'}}) := \mathbf{W}_{gc2}*\Big( \sigma \left[ \mathbf{W}_{gc1}* \mathbf{\Upsilon}_g + \mathbf{b}_{gc1} \right] \Big) + \mathbf{b}_{gc2} + \left[ \mathbf{W}_{gc} \odot \mathbf{Z} + \mathbf{b}_{gc} \right] ~\textcolor{blue}{+} \] \[ \qquad \qquad \qquad \left[ \mathbf{W}_{lc} \odot \mathbf{\hat{Z}} + \mathbf{b}_{lc} \right] + \mathbf{W}_{lc2}*\Big( \sigma \left[ \mathbf{W}_{lc1}* \mathbf{\Upsilon}_l + \mathbf{b}_{lc1} \right] \Big) + \mathbf{b}_{lc2} ~~\textcolor{blue}{+} \] \[ \mathbf{W}_{hfc2}*\Big( \sigma \left[ \mathbf{W}_{hfc1}* \mathbf{Z^{'}} + \mathbf{b}_{hfc1} \right] \Big) + \mathbf{b}_{hfc2}, \]
Both kernel integrals, \(\mathcal{K}_g\) and \(\mathcal{K}_l\), are spectral convolutions: they transform their input with the FFT, multiply a chosen set of frequencies by learned weights, and transform back. \(\mathcal{K}_g\) acts on the full field and keeps only a few low frequencies, while \(\mathcal{K}_l\) acts on each patch and keeps all of them. Choosing that set is plain array slicing, and it only makes sense once you know where each frequency is stored. The interactive figures below show that layout in 2D and 3D.
For a real input of size \(N_x \times N_y\), torch.fft.rfft2 returns \(N_x \times (N_y/2 + 1)\) complex coefficients. Its two axes are stored differently.
The consequence: on a full axis, the low frequencies are not one contiguous block. They live at both ends of the array.
To keep the lowest \(m_1\) frequencies of the full axis and the lowest \(m_2\) of the half axis, a 2D spectral convolution takes one block from each end of the full axis and gives each block its own weight:
x_ft = torch.fft.rfft2(x) # [batch, channels, Nx, Ny//2 + 1]
out_ft[:, :, :m1, :m2] = mul(x_ft[:, :, :m1, :m2], weights1) # low +kx
out_ft[:, :, -m1:, :m2] = mul(x_ft[:, :, -m1:, :m2], weights2) # low −kx
x = torch.fft.irfft2(out_ft) # every other slot stays zero
Use the sliders to change the grid and the number of modes. Each kept slot is coloured by the weight that multiplies it.
The two corners are separate blocks as long as \(2 m_1 \le N_x\); at \(m_1 = N_x/2\) they tile the full axis exactly. The local branch of LOGLO-FNO goes one step further: on each \(P_s \times P_s\) patch it keeps every frequency. Nothing is truncated, so there is nothing to split into corners. The whole patch spectrum is one block, and a single weight multiplies it:
x_ft = torch.fft.rfft2(patches) # [patches, channels, Ps, Ps//2 + 1], all modes
out_ft = mul(x_ft, weight) # one weight over the whole spectrum
patches = torch.fft.irfft2(out_ft)
Choose “Local branch” in the figure above to see this case.
An rfft over three axes gives two full axes and one half axis. Low frequencies sit at both ends of each full axis and at the start of the half axis, so there are \(2 \times 2 \times 1 = 4\) corner blocks, one per weight:
x_ft = torch.fft.rfftn(x, dim=[-3, -2, -1]) # [batch, channels, Nx, Ny, Nz//2 + 1]
out_ft[:, :, :m1, :m2, :m3] = mul(x_ft[:, :, :m1, :m2, :m3], weights1) # +kx, +ky
out_ft[:, :, -m1:, :m2, :m3] = mul(x_ft[:, :, -m1:, :m2, :m3], weights2) # −kx, +ky
out_ft[:, :, :m1, -m2:, :m3] = mul(x_ft[:, :, :m1, -m2:, :m3], weights3) # +kx, −ky
out_ft[:, :, -m1:, -m2:, :m3] = mul(x_ft[:, :, -m1:, -m2:, :m3], weights4) # −kx, −ky
If all three axes were full, there would be \(2^3 = 8\) corners. Because the input is real, the half axis needs only its starting block, which halves the count. In general, \(d\) spatial dimensions give \(2^{d-1}\) corners.
Choose “Local branch”: with every mode of the patch kept, the four corners merge into a single block covering the whole volume, so the local branch uses one weight instead of four.
Both branches of LOGLO-FNO use spectral convolutions, at two very different settings.
The channel mixing inside a spectral convolution costs \(C_{\text{in}} \cdot C_{\text{out}}\) multiply-adds per kept slot, so the number of kept slots \(K\) is what decides its cost. For an \(N_x \times N_y = 128 \times 128\) field:
| Branch | Weight blocks | Kept slots K |
|---|---|---|
| Global branch, 12 × 12 modes | 2 corners of 12 × 12 | 288 |
| Local branch, 16 × 16 patches | 1 block of 16 × 9, shared by 64 patches | 9,216 |
The local count barely depends on the patch size: \(M = N_x N_y / P_s^2\) patches, each with \(P_s (P_s/2 + 1)\) slots, comes to about \(N_x N_y / 2\), roughly every slot of the whole field. So the local branch, not the global one, dominates the cost of the channel mixing, while its FFTs are the cheaper ones, as the complexity analysis below shows.
[:m1] and [-m1:]. The two blocks are disjoint only if \(2 m_1 \le N_x\).[:m2], with \(m_2 \le N_y/2 + 1\). There is no negative block.Let \(N_b\) be the batch size, \(N_x\) and \(N_y\) the resolutions of the spatial dimensions, \(N_c\) be the width or the number of hidden channels, and \(C_{\text{in}}\) and \(C_{\text{out}}\) the numbers of input and output channels, typically set to the same value (e.g., 128). \[ \text{FLOPs}_{\text{FFT}} = 5 \cdot N_b \cdot C_{\text{in}} \cdot N_x \cdot N_y \cdot \log_2(N_x \cdot N_y) \] \[ \text{FLOPs}_{\text{IFFT}} = 5 \cdot N_b \cdot C_{\text{out}} \cdot N_x \cdot N_y \cdot \log_2(N_x \cdot N_y) \] Therefore, FFT computation on the global branch with the full 2D spatial resolution has a per channel complexity of $$\mathcal{O} \Big( N_x \cdot N_y \cdot \log_2(N_x \cdot N_y) \Big),$$ making it expensive for large spatial resolutions such as \(2048\times2048\) or higher.
Let \(M = \frac{N_x \cdot N_y}{P_s^2}\) be the number of patches, \(N_x\) and \(N_y\) the resolutions of the spatial dimensions, \(P_s \times P_s\) the patch size (e.g., \(16 \times 16\)), \(N_c\) be the width or the number of hidden channels, and \(C_{\text{in}}\) and \(C_{\text{out}}\) the numbers of input and output channels, typically set to the same value (e.g., 128). \begin{align*} \text{FLOPs}_{\text{FFT}} &= 5 \cdot N_b \cdot C_{\text{in}} \cdot M \cdot P_s \cdot P_s \cdot \log_2(P_s \cdot P_s) \\ &= 5 \cdot N_b \cdot C_{\text{in}} \cdot N_x \cdot N_y \cdot \log_2(P_s \cdot P_s) \end{align*} \begin{align*} \text{FLOPs}_{\text{IFFT}} &= 5 \cdot N_b \cdot C_{\text{out}} \cdot M \cdot P_s \cdot P_s \cdot \log_2(P_s \cdot P_s) \\ &= 5 \cdot N_b \cdot C_{\text{out}} \cdot N_x \cdot N_y \cdot \log_2(P_s \cdot P_s) \end{align*} Thus, the FFT and IFFT computations on the local branch, which is operating on the patches has a per channel computational complexity of $$\mathcal{O} \Big( N_x \cdot N_y \cdot \log_2(P_s \cdot P_s)\Big).$$ Since, in practice, $$\mathcal{O}\Big(N_x \cdot N_y \cdot \log_2(P_s \cdot P_s)\Big) \ll \mathcal{O}\Big(N_x \cdot N_y \cdot \log_2(N_x \cdot N_y)\Big),$$ the FFT computations are significantly cheaper in the local branch. Moreover, it is highly parallelizable when computing FFTs since each patch can be processed independently, leveraging modern accelerators such as GPUs, TPUs, and other forms of processing units.
Let \(N_b\) be the batch size, \(N_x\), \(N_y\), and \(N_z\) the resolutions of the spatial dimensions, \(N_c\) be the width or the number of hidden channels, and \(C_{\text{in}}\) and \(C_{\text{out}}\) the numbers of input and output channels, typically set to the same value (e.g., 128). \[ \text{FLOPs}_{\text{FFT}} = 5 \cdot N_b \cdot C_{\text{in}} \cdot N_x \cdot N_y \cdot N_z \cdot \log_2(N_x \cdot N_y \cdot N_z) \] \[ \text{FLOPs}_{\text{IFFT}} = 5 \cdot N_b \cdot C_{\text{out}} \cdot N_x \cdot N_y \cdot N_z \cdot \log_2(N_x \cdot N_y \cdot N_z) \] Therefore, FFT computation on the global branch with the full 3D spatial resolution has a per channel complexity of $$\mathcal{O}\Big(N_x \cdot N_y \cdot N_z \cdot \log_2(N_x \cdot N_y \cdot N_z)\Big),$$ making it highly expensive for large values of \(N_x\), \(N_y\), and \(N_z\) such as \(512\times512\times512\) or further higher spatial resolutions.
Let \(M = \frac{N_x \cdot N_y \cdot N_z}{P_s^3}\) be the number of patches, \(N_x\), \(N_y\), and \(N_z\) the resolutions of the spatial dimensions, \(P_s \times P_s \times P_s\) the patch size (e.g., \(16 \times 16 \times 16\), \(32 \times 32 \times 32\), etc.), \(N_c\) be the width or the number of hidden channels, and \(C_{\text{in}}\) and \(C_{\text{out}}\) the numbers of input and output channels, typically set to the same value (e.g., 128). \begin{align*} \text{FLOPs}_{\text{FFT}} &= 5 \cdot N_b \cdot C_{\text{in}} \cdot M \cdot P_s \cdot P_s \cdot P_s \cdot \log_2(P_s \cdot P_s \cdot P_s) \\ &= 5 \cdot N_b \cdot C_{\text{in}} \cdot N_x \cdot N_y \cdot N_z \cdot \log_2(P_s \cdot P_s \cdot P_s) \end{align*} \begin{align*} \text{FLOPs}_{\text{IFFT}} &= 5 \cdot N_b \cdot C_{\text{out}} \cdot M \cdot P_s \cdot P_s \cdot P_s \cdot \log_2(P_s \cdot P_s \cdot P_s) \\ &= 5 \cdot N_b \cdot C_{\text{out}} \cdot N_x \cdot N_y \cdot N_z \cdot \log_2(P_s \cdot P_s \cdot P_s) \end{align*} Thus, the FFT and IFFT computations on the local branch operating on 3D patches has a per channel computational complexity of $$\mathcal{O}\Big(N_x \cdot N_y \cdot N_z \cdot \log_2(P_s \cdot P_s \cdot P_s)\Big).$$ Since, in practice, $$\mathcal{O}\Big(N_x \cdot N_y \cdot N_z \cdot \log_2(P_s \cdot P_s \cdot P_s)\Big) \ll \mathcal{O}\Big(N_x \cdot N_y \cdot N_z \cdot \log_2(N_x \cdot N_y \cdot N_z)\Big),$$ the FFT computations are significantly cheaper in the local branch. Furthermore, it is highly parallelizable when computing FFTs since each patch can be processed independently, leveraging modern accelerators such as GPUs, TPUs, and other forms of PUs.
Plugging concrete sizes into the formulas above: both branches transform every grid point, so their FFT FLOPs differ only in the log factor, \(\log_2(N_x \cdot N_y)\) for one FFT over the whole field against \(\log_2(P_s \cdot P_s)\) for each patch (with \(N_z\) and a third \(P_s\) in 3D). On a grid with \(N_x = N_y \,(= N_z)\), the local branch therefore needs \(\log_2 N_x / \log_2 P_s\) times fewer FFT FLOPs, and the gap widens as the resolution grows while the patch size stays fixed. The inverse FFT costs the same again in both branches.
Batch size \(N_b = 16\) and \(C_{\text{in}} = 64\) channels; both branches scale with them in the same way, so the ratio does not depend on them.
In addition, we propose a spectral loss term based on the radial binning of spectral energy of errors, which is as follows:
def RadialBinnedSpectralLoss(preds, target):
# input data shape and params
nb, nc, nx, ny, nt = target.size()
iLow, iHigh = 4, 12
Lx, Ly = 1.0, 1.0
# Compute error in Fourier space
err_phys = preds - target
err_fft = torch.fft.fftn(err_phys, dim=[2, 3])
err_fft_sq = torch.abs(err_fft)**2
err_fft_sq_h = err_fft_sq[Ellipsis, :nx//2, :ny//2, :]
# Create radial indices
x = torch.arange(nx//2)
y = torch.arange(ny//2)
X, Y = torch.meshgrid(x, y, indexing="ij")
radii = torch.sqrt(X**2 + Y**2).floor().to(torch.int) # Radial dist.
max_radius = int(torch.max(radii))
# flatten radii for binary mask
radii_flat = radii.flatten() # (nx//2 * ny//2)
# Spatially flatten Fourier space error; (nb, nc, nx//2 * ny//2, nt)
err_fft_sq_flat = err_fft_sq_h.contiguous().reshape(nb, nc, -1, nt)
# initialize output tensor to hold the Fourier error
# for each radial bin at distance r from the origin
err_F_vect_full = torch.zeros(nb, nc, max_radius + 1, nt)
# Apply ‘index_add_‘ for all radii and accumulate the errors
valid_r = radii_flat <= max_radius # binary mask to find valid radii
# Sum for all valid radial indices
err_F_vect_full.index_add_(2,
radii_flat[valid_r],
err_fft_sq_flat[:, :, valid_r]
)
# Normalize & compute mean over batch; (nc, min(nx//2, ny//2), nt)
nrm = (nx * ny) * Lx * Ly
_err_F = torch.sqrt(torch.mean(err_F_vect_full, dim=0)) / nrm
# Classify Fourier space error into three bands
err_F = torch.zeros([nc, 3, nt])
err_F[:, 0] += torch.mean(_err_F[:, :iLow], dim=1) # low freqs
err_F[:, 1] += torch.mean(_err_F[:, iLow:iHigh], dim=1) # mid freqs
err_F[:, 2] += torch.mean(_err_F[:, iHigh:], dim=1) # high freqs
# mean or sum over the channels and time dimensions
if reduction == "mean":
freq_loss = torch.mean(err_F, dim=[0, -1])
elif reduction == "sum":
freq_loss = torch.sum(err_F, dim=[0, -1])
return freq_loss
The 1-step training loss for \(N\) trajectories, each comprising \(T\) timesteps, is given by,
where \(\mathcal{C}_{\mathrm{MSE}}\) is the mean squared error and \(\mathcal{C}_{\mathrm{freq}}\) is the radially binned spectral loss of Algorithm 1, computed by RadialBinnedSpectralLoss in the pseudocode above.
Let \(\mathbf{X}^{\mathrm{hf}} \in \mathbb{R}^{N_b \times N_x \times N_y \times (N_t \cdot N_c)}\) denote the input tensor of HF features, where \(N_b\) is the batch size, \(N_x\) and \(N_y\) are the resolutions of the spatial dimensions, and \(N_t \cdot N_c\) represents the combined temporal and channel dimensions. The high-frequency feature adaptive Gaussian noise \(\mathbf{N}_{\mathrm{dynamic}}\) is then computed as follows:
1. Compute (per sample) Mean \(\mu_b\) and Standard Deviation \(\sigma_b\) of High-Frequency Features \[ \mu_b = \frac{1}{N_x \cdot N_y \cdot N_t \cdot N_c} \sum_{i=1}^{N_x} \sum_{j=1}^{N_y} \sum_{k=1}^{N_t N_c} \mathbf{X}_{b,i,j,k}^{\mathrm{hf}} \] \[ \sigma_b = \sqrt{\frac{1}{N_x \cdot N_y \cdot N_t \cdot N_c} \sum_{i=1}^{N_x} \sum_{j=1}^{N_y} \sum_{k=1}^{N_t N_c} (\mathbf{X}_{b,i,j,k}^{\mathrm{hf}} - \mu)^2} + \epsilon \] where \(\epsilon\) is a small constant added for numerical stability, and \(\mu\) and \(\sigma\) are obtained by stacking the per sample statistics along the batch dimension. 2. Generate Standard Gaussian Noise \[ \mathbf{N} \sim \mathcal{N}(0, 1) \] 3. Scale Noise Dynamically \[ \mathbf{N}_{\mathrm{dynamic}} = \mu + \alpha \cdot \sigma \cdot \mathbf{N} \] where \(\alpha\) is a small value such as 0.025 and \(\mathbf{N}_{\mathrm{dynamic}}\) has the same shape as the input \(\mathbf{X}^{\mathrm{hf}}\). \(\mathbf{N}_{\mathrm{dynamic}}\) can now be added to the batch of inputs to the global and local branches during the training phase of LOGLO-FNO.In the below slideshow, we visualize the radially binned spectral energy errors of predictions of the considered neural operators and LOGLO-FNO on the Kolmogorov Flow 2D PDE. Note that we show only alternate radial bins prioritizing uncluttered representation over completeness.
We evaluate LOGLO-FNO on the challenging turbulent version of Kolmogorov Flow 2D benchmark
We evaluate LOGLO-FNO on the challenging setup of Turbulent Radiative Mixing Layer 3D benchmark
The setup comprises training with 1-step loss and evaluating 1-step results on a host of metrics. The results are compared against a diverse set of competitive neural operator baselines such as Modern UNet, ConvNext U-Net, and FNO.
We evaluate LOGLO-FNO on the challenging coupled PDE, Diffusion Reaction 2D, benchmark
We visualize the predictions of FNO and LOGLO-FNO on the time-dependent Turbulent Radiative Mixing Layer 3D PDE.
@inproceedings{loglo-fno-kalimuthu:2025,
title={{LOGLO}-{FNO}: Efficient Learning of Local and Global Features in Fourier Neural Operators},
author={Marimuthu Kalimuthu and David Holzm{\"u}ller and Mathias Niepert},
journal={Transactions on Machine Learning Research},
issn={2835-8856},
year={2025},
url={https://openreview.net/forum?id=MQ1dRdHTpi},
note={J2C Certification}
}